[med-svn] [python-pbcore] branch upstream updated (cd3bf35 -> 0d7b8ea)

[Afif Elghraoui]

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afif-guest pushed a change to branch upstream
in repository python-pbcore.

      from  cd3bf35   Imported Upstream version 1.2.2+dfsg1
       new  0d7b8ea   Imported Upstream version 1.2.3+dfsg

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Summary of changes:
 CHANGELOG.org                                      |     6 +
 bin/dataset.py                                     |     3 +
 doc/pacbio-theme/static/headerGradient.jpg         |   Bin 0 -> 7099 bytes
 doc/pacbio-theme/static/pacbio.css                 |   238 +
 doc/pacbio-theme/static/pacbioLogo.png             |   Bin 0 -> 3128 bytes
 doc/pacbio-theme/static/pygments.css               |    55 +
 doc/pacbio-theme/theme.conf                        |     4 +
 pbcore/__init__.py                                 |     2 +-
 pbcore/data/Makefile                               |    28 +-
 pbcore/data/__init__.py                            |     3 +
 pbcore/data/datasets/__init__.py                   |    20 +-
 pbcore/data/datasets/alignment.dataset.xml         |   157 +-
 pbcore/data/datasets/barcode.dataset.xml           |    39 +-
 pbcore/data/datasets/ccsaligned.dataset.xml        |    48 +
 pbcore/data/datasets/ccsread.dataset.xml           |    61 +-
 pbcore/data/datasets/contig.dataset.xml            |    54 +-
 pbcore/data/datasets/fofn.fofn                     |     2 +-
 pbcore/data/datasets/lambda.alignmentset.xml       |    15 +
 pbcore/data/datasets/lambda.pbalign.xml            |     2 -
 pbcore/data/datasets/lambda.reference.xml          |     2 -
 pbcore/data/datasets/lambda.referenceset.xml       |    19 +
 pbcore/data/datasets/pbalchemysim.alignmentset.xml |    57 +
 .../data/datasets/pbalchemysim.hdfsubreadset.xml   |    11 +
 pbcore/data/datasets/pbalchemysim.pbalign.xml      |     2 -
 .../pbalchemysim0.alignmentset.chunk0contigs.xml   |    47 +
 .../pbalchemysim0.alignmentset.chunk1contigs.xml   |    47 +
 .../data/datasets/pbalchemysim0.alignmentset.xml   |    15 +
 .../data/datasets/pbalchemysim0.hdfsubreadset.xml  |    10 +
 pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi |   Bin 2115 -> 2147 bytes
 .../pbalchemysim0.pbalign.chunk0contigs.xml        |     2 -
 .../pbalchemysim0.pbalign.chunk1contigs.xml        |     2 -
 pbcore/data/datasets/pbalchemysim0.pbalign.xml     |     2 -
 pbcore/data/datasets/pbalchemysim0.reference.xml   |    77 -
 .../data/datasets/pbalchemysim0.referenceset.xml   |    77 +
 pbcore/data/datasets/pbalchemysim0.subread.xml     |     2 -
 .../data/datasets/pbalchemysim0.subreads.bam.bai   |   Bin 0 -> 16 bytes
 .../data/datasets/pbalchemysim0.subreads.bam.pbi   |   Bin 0 -> 1003 bytes
 pbcore/data/datasets/pbalchemysim0.subreadset.xml  |    10 +
 .../data/datasets/pbalchemysim1.alignmentset.xml   |    15 +
 .../data/datasets/pbalchemysim1.hdfsubreadset.xml  |    10 +
 pbcore/data/datasets/pbalchemysim1.pbalign.xml     |     2 -
 pbcore/data/datasets/pbalchemysim1.subread.xml     |     2 -
 .../data/datasets/pbalchemysim1.subreads.bam.bai   |   Bin 0 -> 16 bytes
 .../data/datasets/pbalchemysim1.subreads.bam.pbi   |   Bin 0 -> 945 bytes
 pbcore/data/datasets/pbalchemysim1.subreadset.xml  |    10 +
 pbcore/data/datasets/reference.dataset.xml         |    69 +-
 pbcore/data/datasets/subread.dataset.xml           |  1014 +-
 pbcore/data/datasets/subreadSetWithStats.xml       |  2262 ++-
 .../datasets/transformed_rs_subread.dataset.xml    |   152 +-
 pbcore/data/empty.ccs.bam                          |   Bin 0 -> 540 bytes
 pbcore/data/empty.ccs.bam.pbi                      |   Bin 0 -> 67 bytes
 pbcore/io/BasH5IO.py                               |    18 +-
 pbcore/io/GffIO.py                                 |    64 +
 pbcore/io/align/BamAlignment.py                    |    29 +-
 pbcore/io/align/BamIO.py                           |     5 +-
 pbcore/io/align/PacBioBamIndex.py                  |     2 +-
 pbcore/io/align/_bgzf.py                           |    55 +-
 pbcore/io/dataset/DataSetIO.py                     |  2898 ++--
 pbcore/io/dataset/DataSetMembers.py                |   191 +-
 pbcore/io/dataset/DataSetReader.py                 |   100 +-
 pbcore/io/dataset/DataSetValidator.py              |     2 +
 pbcore/io/dataset/DataSetWriter.py                 |   145 +-
 pbcore/io/dataset/DataSetXsd.py                    | 13884 ++-----------------
 pbcore/io/dataset/EntryPoints.py                   |    63 +-
 pbcore/io/dataset/_pbbase.py                       |  4563 ++++++
 pbcore/io/dataset/_pbds.py                         |  3435 +++++
 pbcore/io/dataset/_pbmeta.py                       |  2056 +++
 pbcore/io/dataset/_pbpn.py                         |   507 +
 pbcore/io/dataset/_pbrk.py                         |  1218 ++
 pbcore/io/dataset/_pbsample.py                     |   632 +
 pbcore/io/dataset/utils.py                         |   125 +
 tests/test_pbcore_io_AlnFileReaders.py             |     9 +
 tests/test_pbcore_io_GffIO.py                      |    67 +-
 tests/test_pbcore_io_bgzf.py                       |    42 +
 tests/test_pbdataset.py                            |   389 +-
 tests/test_pbdataset_subtypes.py                   |   319 +-
 76 files changed, 19382 insertions(+), 16091 deletions(-)
 create mode 100644 doc/pacbio-theme/static/headerGradient.jpg
 create mode 100644 doc/pacbio-theme/static/pacbio.css
 create mode 100644 doc/pacbio-theme/static/pacbioLogo.png
 create mode 100644 doc/pacbio-theme/static/pygments.css
 create mode 100644 doc/pacbio-theme/theme.conf
 create mode 100644 pbcore/data/datasets/ccsaligned.dataset.xml
 create mode 100644 pbcore/data/datasets/lambda.alignmentset.xml
 delete mode 100644 pbcore/data/datasets/lambda.pbalign.xml
 delete mode 100644 pbcore/data/datasets/lambda.reference.xml
 create mode 100644 pbcore/data/datasets/lambda.referenceset.xml
 create mode 100644 pbcore/data/datasets/pbalchemysim.alignmentset.xml
 create mode 100644 pbcore/data/datasets/pbalchemysim.hdfsubreadset.xml
 delete mode 100644 pbcore/data/datasets/pbalchemysim.pbalign.xml
 create mode 100644 pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml
 create mode 100644 pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml
 create mode 100644 pbcore/data/datasets/pbalchemysim0.alignmentset.xml
 create mode 100644 pbcore/data/datasets/pbalchemysim0.hdfsubreadset.xml
 delete mode 100644 pbcore/data/datasets/pbalchemysim0.pbalign.chunk0contigs.xml
 delete mode 100644 pbcore/data/datasets/pbalchemysim0.pbalign.chunk1contigs.xml
 delete mode 100644 pbcore/data/datasets/pbalchemysim0.pbalign.xml
 delete mode 100644 pbcore/data/datasets/pbalchemysim0.reference.xml
 create mode 100644 pbcore/data/datasets/pbalchemysim0.referenceset.xml
 delete mode 100644 pbcore/data/datasets/pbalchemysim0.subread.xml
 create mode 100644 pbcore/data/datasets/pbalchemysim0.subreads.bam.bai
 create mode 100644 pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi
 create mode 100644 pbcore/data/datasets/pbalchemysim0.subreadset.xml
 create mode 100644 pbcore/data/datasets/pbalchemysim1.alignmentset.xml
 create mode 100644 pbcore/data/datasets/pbalchemysim1.hdfsubreadset.xml
 delete mode 100644 pbcore/data/datasets/pbalchemysim1.pbalign.xml
 delete mode 100644 pbcore/data/datasets/pbalchemysim1.subread.xml
 create mode 100644 pbcore/data/datasets/pbalchemysim1.subreads.bam.bai
 create mode 100644 pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi
 create mode 100644 pbcore/data/datasets/pbalchemysim1.subreadset.xml
 create mode 100644 pbcore/data/empty.ccs.bam
 create mode 100644 pbcore/data/empty.ccs.bam.pbi
 create mode 100755 pbcore/io/dataset/_pbbase.py
 create mode 100755 pbcore/io/dataset/_pbds.py
 create mode 100755 pbcore/io/dataset/_pbmeta.py
 create mode 100755 pbcore/io/dataset/_pbpn.py
 create mode 100755 pbcore/io/dataset/_pbrk.py
 create mode 100755 pbcore/io/dataset/_pbsample.py
 create mode 100755 pbcore/io/dataset/utils.py
 create mode 100644 tests/test_pbcore_io_bgzf.py

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